This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. SUMMARY: Qvality is a C++ program for estimating two types of standard statistical confidence measures: the q value, which is an analog of the p value that incorporates multiple testing correction, and the posterior error probability (PEP, also known as the local false discovery rate), which corresponds to the probability that a given observation is drawn from the null distribution. In computing q values, Qvality employs a standard bootstrap procedure to estimate the prior probability of a score being from the null distribution;for PEP estimation, Qvality relies upon nonparametric logistic regression. Relative to other tools for estimating statistical confidence measures, Qvality is unique in its ability to estimate both types of scores directly from a null distribution, without requiring the user to calculate p values. AVAILABILITY: A web server, C++ source code and binaries are available under MIT license at http://noble.gs.washington.edu/proj/qvality.